GWAS of Helicobacter. pylori serologic status
Overview of H.Pylori Helicobacter pylori is a Gram negative, micoaerophilic, flagellated (motile) bacterium that has tropism toward gastric epithelium. Survives within narrow pH range (requires acid environment, secretes urease), causes mucosal damage via cytotoxicity and inflammatory response. H.pylori was Discovery by Barry Marshall and he won a Nobel Prize 2005, for his work. H. pylori is the leading cause of peptic ulcer disease(PUD), accounts for 70-80% reported cases of gastritis and gastroduodenal ulcer disease in U.S. Common lifetime risk 10% 500,000 new cases yearly. Peptic ulcer is a necrotic disruption of the mucosal epithelial layer with extension into the submucosa. Pathogenesis/potential disease mechanism of peptic ulcer by H.pylori, involves altered gastric acid secretion, decrease mucin secretion, loss of mucus-bicarbonate barrier, increase pepsinogen secretion, acid-pepsin injury, and regional ischemia. Eradication involves antibiotics combination (Amoxicillin+clarithromycin), and Proton pump inhibitor (Omeprazole) (Katzung B, et.al., 2012). H.pylori susceptibility has been hypothesized to be associated with genetic variation. In order to identify the genetic loci associated with H. pylori seroprevalence a two independent cohort study was conducted.Julia Mayerle and colleagues, to identify genetic loci associated with H. pylori seroprevalence, two independent population-based cohorts was conducted; also to ascertain their “pathophysiological role by whole blood RNA gene expression profiling.” According to a report published in the Journal of the American Medical Association, they reported after a meta-analysis that there “is an association between TLR1 and H. pylori seroprevalence, a finding that requires replication in non-white populations. If confirmed, genetic variations in TLR1 may help explain some of the observed variation in individual risk for H. pylori infection” (Mayerle J., e.t., 2013). METHODS Study Cohorts In order to identify genetic loci associated with H. pylori seroprevalence, SHIP (Study of Health in Pomerian) conducted two independent white population-based cohorts (SHIP in October 1997 to May 2001 and SHIP-trend September 2008 and summer 2012), in Northeast Germany. The aim of SHP and SHIP-trend study was to (1) assess prevalence and incidence of common risk factors, subclinical disorders, and clinical diseases. (2) Investigate the complex associations among risk factors, subclinical disorders, and clinical diseases.An addition study was conducted in Rotterdam, a white elderly based population of European ancestry composed of three cohorts (RS-I obtains 1990 and 1993, RS-II established in 2000-2001and RS-III started in 2006 and the recruitment ended in 2008); that have cardiovascular,endocrine, hepatic, neurologic, ophthalmic, psychiatric, and respiratory diseases. The study is limited to the individuals residing in a Rotterdam, the Netherlands. A meta-analysis of the data was studied by GWASs Phenotype Determination: Seroprevalence and Bacteria load A measurement of Anti-H pylori serum IgG antibody titer was taking using commercial enzyme immunoassays (Pyloriset EIA-G III ELISA; Orion).Seroprevalence is litmus for current or previous infection, an anti–H pylori IgG titer equal to or greater than 20 U/mL. This method of serological testing of H pylori infection has a sensitivity value of 97.8%, a specificity of 58.0%, and an accuracy of 78.7%. 71.5% is a positive benchmark for the Pyloriset EIA-G III ELISA immunoassay and 96.2% for the negative predictive value. Infection is predicted based on a correlation between titre level of gene expression and fecal H pylori antigen titer. The control group comprises of the individuals with the lowest 75% IgG titer distribution. “Individuals with high bacterial load (based on fecal H pylori antigen titer, optical density OD>1) were studied to determine if they also exhibited the highest 25% of gene expression levels of the respective 4p14-region genes” (Mayerle J., et.al 2013). ELISA kit was used to detect positive fecal H pylori antigen, with a sensitivity value of 97.7% and specificity as 96.3%. RESULTS Prevalence and Frequency of H.pylori Seroprevalence Of the 10938 participants, 6160 (56.3%) (SHIP, RS-I, RS-II) and indicated some level of Seroprevalence. “'''Based on the predefined phenotypic seroprevalence in the top 25% of the study population, a total of 2623 cases (25%) and 7862 controls (75%) were used for GWAS meta-analysis (SHIP, RS-I, and RS-II)”'(Mayerle J., et.al 2013) . In order to ensure increase specificity and decrease false-positive H pylori infections in the case group of the GWAS, upper 25% of the IgG titer distribution of the corresponding cohort (124.5 U/mL for SHIP, 136.8 U/mL for RS-I, and 88.9 U/mL for RS-II) was set as the cutoff point. GWAS Meta- analysis Two genome-wide significant loci were identified using a Meta analysis of data from RS-I, RS-II, and SHIP (n = 10 485, for which H pylori serology and genotyping data were available). TLR locus on 4p14 exhibited the lowest P value with rs10004195 ''rs10004195 as the lead SNP (odds ratio OR for the minor allele, 0.70 CI, 0.65-0.76; P = 1.42 × 10−18; MAF = 24.7%), closely followed by rs4833095 ''(OR for the minor allele, 0.70 CI, 0.65-0.76; P = 1.43 × 10−18; MAF = 24.9%). “Second genome-wide significant locus was located on chromosome 1q23.3, with P = 2.1 × 10−8 for the lead SNP, ''rs368433 ''(OR for the minor allele, 0.73 CI, 0.65-0.81; MAF = 16%). For rs10004195 the association P value increased to 6.5 × 10−9 using this model, and the combined effect estimate was nearly the same (OR, 0.69 CI, 0.61-0.79), indicating that the observed association was not completely driven by a single study. For SNP rs368433, the association P value and combined effect size were essentially unchanged compared with the fixed-effects meta-analysis (OR, 0.73 CI, 0.65-0.82; P = 9.2 × 10−8), but the P value no longer met the genome-wide significance threshold”(Mayerle J., et.al 2013) . Genome-wide significant SNPs Analysis of 1000 genomes database using the SNAP SNP Proxy search tool, revel 2 nonsynonymous SNPs in ''TLR1 ''and 1 SNP in ''TLR10 in linkage disequilibrium with the top-ranked SNP (rs10004195). In TLR1, rs4833095 (r''2 = 1.0) and ''rs5743618 (r''2 = 0.95) are nonsynonymous SNPs. rs4833095 causes the amino acid substitution Asn248Ser, rs5743618 results in the Ser602Ile substitution. Close to the 3′ end of the single protein–coding exon of the gene is the ''TLR10, rs4129009 (r''2 = 0.77), corresponding to the Ile775Val substitution. The position of TLR10 amino acid is “localized within the intracellular TIR (toll/interleukin-1 receptor) domain that participates in the transduction of extracellular signaling.” DISCUSSION Two genome-wide significant loci located at 4p14 and 1q23.3 was identified by GWAS that are associated with H pylori seroprevalence. The 4p14 region codes for have three different genes, the TLR1, TLR6, and TLR10 genes. H pylori seroprevalence was associated with TLR1 as the most like causative receptor. TLRs are also known to function as a protective immunity against infection. Murine models have previously suggested that TLR2 represents the only cell surface receptor/ligand system that can cause a significant anti-inflammatory effect.TLR1, one of the coreceptors of TLR2, can form a heterodimer that are speculated to recognize triacylated lipopeptides from the cell envelope of H pylori lipid A. TLR1 has also been linked to have an effect in ''Chlamydia and leprosy infection; in a recent study that showed the association of rs5743618, a nonsynonymous SNP in linkage with rs10004195 identified in this study. The 1q23.3 region was also significantly associated with the H pylori phenotype, based on GWAS meta-analysis. “The minor allele of the top-ranked SNP, rs368433, was associated with low anti–H pylori IgG titers, decreased blood levels of HSPA6 and FCGR2A, and increased expression levels of FCGR2B. The FCGR2B-encoded Fcy receptor IIB also seems plausibly related to seroprevalence, because genetic variations affecting the receptor's affinity for IgG subclass 2 (IgG2) have been reported” (Mayerle J., et.al 2013). GWAS meta-analysis identified an association between TLR1 and H pylori seroprevalence, but the study have some limitation and requires replication in nonwhite independent population. Some of the limitation of study includes: (1) the study was conducted among participants phenotyped only for seroprevalence and not symptomatic H pylori infection (2) the validity of the current results are restricted to individuals of European ancestry and (3) reproducibility of same result is uncertain in a cohort exposed to a significantly higher pathogen pressure. REFERENCES El-Omar EM. Helicobacter pylori Susceptibility in the GWAS Era. ''JAMA. ''2013;309(18):1939-1940. doi:10.1001/jama.2013.5590 Katzung, B., Masters, S., & Trevor, A. (2012). Drugs Used in the Treatment of GI diseases. In Katzung Basic and Clinical Pharmacology 12th edition (2012) (12th ed., p. 1100). The McGraw-Hill Companies. Mayerle J, den Hoed CM, Schurmann C, et al. Identification of Genetic Loci Associated With Helicobacter pylori Serologic Status. ''JAMA. ''2013;309(18):1912-1920. doi:10.1001/jama.2013.4350. Wurfel MM, Hawn TR. Genetic Variants Associated With Susceptibility to Helicobacter pylori. ''JAMA. ''2013;310(9):976. doi:10.1001/jama.2013.194762